On Mon, Jul 8, 2013 at 9:14 PM, Ross Lazarus <ross.laza...@channing.harvard.edu> wrote: > Hi, Bioconductor devs, > > In very rare cases (eg > http://article.gmane.org/gmane.science.biology.informatics.conductor/35266/match=update+edgeR) > where BioC package authors have released an urgent bug fix within a given > BioC update cycle, the usual automated biocLite installation process does > not appear to support recreating a very specific R/Bioc environment > containing a precisely specified package release (say the previous edgeR > 2.2.0 fixed by 2.2.5). You might argue a user should never do this, but > since we want truly reproducible analyses (the context is the new toolshed > dependency control mechanisms in Galaxy), we need to control *all* > dependencies for a given release of a (eg edgeR) wrapper at this very fine > level of granularity, acknowledging that reproducible =/= valid. > > Take that edgeR update as a test case. I know about > http://bioconductor.org/checkResults/ and eg > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR/ but I > have been unable to figure out how to track down the 2.2.0 edgeR archive > (or for that matter the 2.2.5 bugfix) - I'm sure it is in svn somewhere. > Any advice on how I can identify a long term reliable svn or other url to > script the download of a specific (even if know buggy) historical archive > of (eg) edgeR 2.2.0? >
In the checked-out edgeR working directory, do: svn log --diff DESCRIPTION > diff.txt (this requires subversion >= 1.7) Then look in diff.txt for "Version: 2.2.0". This ends up being revision 54800. Then you can check that out to a different directory with svn co -r54800 https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR/ Dan For more on the topic you bring up, see the thread started by https://stat.ethz.ch/pipermail/bioconductor/2013-March/051224.html > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
